If you ran barefoot and have a blister, wear something to protect it. Don't run barefoot till it is healed. It is going to be a long grueling process of trial an error to run barefoot without blisters. I have been working at it since August of 09 and I still get blisters when I run. My longest run without blisters was 2 miles, but it left my feet tender.
I did my second barefoot run of about 2 miles again today. I still havent felt any muscular sore or pain at all, but my blisters filled up again. Before my run today they had pretty much healed up. Its lots of fun though. Thanks for the advice.